Question: Generate Heatmap after DEseq2 analysis
0
gravatar for nicolas.hipp
2.6 years ago by
Rennes, France
nicolas.hipp0 wrote:

Hi everyone,

I have a problem to represent my RNAseq data. I have a list of DE genes as output of DEseq2. So I would like to make an heatmap of these genes across all my conditions (3 conditions, and 3 samples per condition)

Problems starts here because I don't really know which values I have to take in input of DEseq2. Can I sort my DE gene-list and perform my heatmap with the values provided by the rlog function of DEseq2?

Sorry for the naive question, maybe i'm totally wrong. Thanks

rna-seq deseq2 • 1.6k views
ADD COMMENTlink modified 2.5 years ago by Nicolas Rosewick7.6k • written 2.6 years ago by nicolas.hipp0

Dear Nicolas, Hi

Please have a look at this Trinity page for "Automatically Partitioning Genes into Expression Clusters" and "Interactive analysis of DE features using MeV".

Maybe that could help.

~ Best

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Farbod3.2k

Hello :) Thanks for the answer, I will have a look on it. Best ;)

ADD REPLYlink written 2.6 years ago by nicolas.hipp0
2
gravatar for Nicolas Rosewick
2.5 years ago by
Belgium, Brussels
Nicolas Rosewick7.6k wrote:

Read the DESeq2 vignette. There is a section regarding heatmaps using transformed data vsd or rld

ADD COMMENTlink written 2.5 years ago by Nicolas Rosewick7.6k
0
gravatar for Ron
2.5 years ago by
Ron930
United States
Ron930 wrote:

You can take the expression values (FPKMS )of those genes in the samples and plot a heat map.

ADD COMMENTlink written 2.5 years ago by Ron930
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 922 users visited in the last hour